Package eu.isas.peptideshaker.stirred

Class Stirred

java.lang.Object
eu.isas.peptideshaker.stirred.Stirred
public class Stirred extends Object
This class imports the results of a search engine from SearchGUI in the utilities model.
Author:
Marc Vaudel

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    final String
    SOFTWARE_NAME
    The name of the software to annotate in the mzIdentML file.
    final String
    SOFTWARE_URL
    The URL of the software to annotate in the mzIdentML file.
    final String
    SOFTWARE_VERSION
    The version of the software to annotate in the mzIdentML file.

  • Constructor Summary

    Constructors
    Constructor
    Description
    Stirred(File inputFile, File spectrumFile, File fastaFile, File ouputFolder, File identificationParametersFile, File tempFolder, com.compomics.software.log.CliLogger cliLogger, int nThreads, int timeOutDays, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail)
    Constructor.

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    process(File searchEngineResultsFile, File fastaFile, File ouputFile, com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex fmIndex, com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary, com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler)
    Runs the stirred process.
    void
    run()
    Runs the stirred process.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Field Details

    • SOFTWARE_NAME

      public final String SOFTWARE_NAME
      The name of the software to annotate in the mzIdentML file.
      See Also:

    • SOFTWARE_VERSION

      public final String SOFTWARE_VERSION
      The version of the software to annotate in the mzIdentML file.

    • SOFTWARE_URL

      public final String SOFTWARE_URL
      The URL of the software to annotate in the mzIdentML file.
      See Also:

  • Constructor Details

    • Stirred

      public Stirred(File inputFile, File spectrumFile, File fastaFile, File ouputFolder, File identificationParametersFile, File tempFolder, com.compomics.software.log.CliLogger cliLogger, int nThreads, int timeOutDays, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail)
      Constructor.
      Parameters:
      inputFile - The input file.
      spectrumFile - The spectrum file.
      fastaFile - The fasta file.
      ouputFolder - The output folder.
      identificationParametersFile - The identification parameters file.
      tempFolder - The temp folder to use for temp files.
      cliLogger - The temp folder to use for temp files.
      nThreads - The number of threads to use.
      timeOutDays - Timeout time in days.
      contactFirstName - The first name of the contact to annotate in the mzIdentML file.
      contactLastName - The last name of the contact to annotate in the mzIdentML file.
      contactAddress - The address of the contact to annotate in the mzIdentML file.
      contactEmail - The email of the contact to annotate in the mzIdentML file.
      contactOrganizationName - The name of the organization of the contact to annotate in the mzIdentML file.
      contactOrganizationAddress - The address of the organization of the contact to annotate in the mzIdentML file.
      contactOrganizationEmail - The email of the organization of the contact to annotate in the mzIdentML file.

  • Method Details

    • run

      public void run() throws InterruptedException, TimeoutException, IOException
      Runs the stirred process.
      Throws:
      InterruptedException - Exception thrown if a thread is interrupted.
      TimeoutException - Exception thrown if the process times out.
      IOException - Exception thrown if an error occurred while reading or writing a file.

    • process

      public void process(File searchEngineResultsFile, File fastaFile, File ouputFile, com.compomics.util.experiment.identification.protein_inference.fm_index.FMIndex fmIndex, com.compomics.util.experiment.io.biology.protein.FastaSummary fastaSummary, com.compomics.util.experiment.io.mass_spectrometry.MsFileHandler msFileHandler, com.compomics.util.parameters.identification.IdentificationParameters identificationParameters, com.compomics.util.waiting.WaitingHandler waitingHandler) throws InterruptedException, TimeoutException, IOException
      Runs the stirred process.
      Parameters:
      searchEngineResultsFile - The search engine results file.
      fastaFile - The fasta file.
      ouputFile - The output file.
      fmIndex - The FM index of the fasta file.
      fastaSummary - The summary information on the fasta file.
      msFileHandler - The mass spectrometry file handler to use.
      identificationParameters - The identification parameters.
      waitingHandler - The waiting handler to use.
      Throws:
      InterruptedException - Exception thrown if a thread is interrupted.
      TimeoutException - Exception thrown if the process times out.
      IOException - Exception thrown if an error occurred while reading or writing a file.